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Fix/hexanoate #717

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merged 8 commits into from
Oct 30, 2023
Merged

Fix/hexanoate #717

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7635dd6
Removed hexanoate, MAM03684c
pranasag Oct 27, 2023
c490f1d
Added missing [x] and [m] species
pranasag Oct 27, 2023
4139c46
Added species MAM02120x and MAM02120m to Human-GEM.yml
pranasag Oct 27, 2023
ca73f3e
Removed deprecated species from the model
pranasag Oct 27, 2023
85203ec
Removed duplicate rxn MAR09949
pranasag Oct 27, 2023
f924ff6
Added BiGG ID for MAM02120
pranasag Oct 29, 2023
373fc6a
Merge branch 'develop' into fix/hexanoate
haowang-bioinfo Oct 29, 2023
d4d0c50
Added GPRs to MAR10377 and MAR10374
pranasag Oct 30, 2023
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4 changes: 4 additions & 0 deletions data/deprecatedIdentifiers/deprecatedMetabolites.tsv
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Expand Up @@ -2254,3 +2254,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM20023i" "MAM20023" "C00061" "" "" "CHEBI:58210" "" "" "" "" "" "MNXM1105928" "" ""
"MAM02398c" "MAM02398" "" "C16238" "" "" "23724672" "" "CE5656" "" "CE5656" "MNXM2392" "m02398c" "m02398c"
"MAM01701c" "MAM01701" "dhlam" "C00579" "HMDB0000985" "CHEBI:17694" "663" "" "" "HC00437" "dhlam" "MNXM1277" "m01701c" "m01701c"
"MAM03684c" "MAM03684" "hxa" "" "" "CHEBI:17120" "" "" "" "" "hxa" "MNXM1653" "" "hxa_c"
"MAM03684m" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_m"
"MAM03684e" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_s"
"MAM03684x" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_p"
3 changes: 3 additions & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Expand Up @@ -256,3 +256,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR06398" "R07770" "" "R07770C" "" "" "RE1944C" "MNXR101081" "HMR_6398" "RCR14489" "" 0 "" "RHEA:12913" "HMR_6398"
"MAR06399" "R07771" "" "R07771C" "" "" "HMR_6399" "MNXR111358" "HMR_6399" "RCR14490" "" 0 "" "RHEA:20473" "HMR_6399"
"MAR06408" "" "" "RT0295" "" "" "HMR_6408" "" "HMR_6408" "RCR21069" "" 0 "" "" "HMR_6408"
"MAR11292" "" "HXAt3" "" "" "" "HXAt3" "" "" "" "" 0 "" "" "HXAt3"
"MAR11293" "" "EX_hxa_e" "" "" "" "EX_hxa[e]" "MNXR98664" "" "" "" 0 "" "" "EX_hxa[e]"
"MAR09949" "" "FACOAE60" "" "" "" "HXCOAc" "MNXR99139" "" "" "" 0 "" "" "HXCOAc"
122 changes: 28 additions & 94 deletions model/Human-GEM.yml
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Expand Up @@ -29241,6 +29241,22 @@
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM02120x"
- name: "hexanoic acid"
- compartment: "x"
- formula: "C6H11O2"
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM02120m"
- name: "hexanoic acid"
- compartment: "m"
- formula: "C6H11O2"
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM02121c"
- name: "hexanoyl-[ACP]"
Expand Down Expand Up @@ -53209,14 +53225,6 @@
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03684c"
- name: "Hexanoate (N-C6:0)"
- compartment: "c"
- formula: "C6H11O2"
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03976c"
- name: "Cia-5,8, Tetradecadienoic Acid"
Expand Down Expand Up @@ -54353,22 +54361,6 @@
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03684m"
- name: "Hexanoate (N-C6:0)"
- compartment: "m"
- formula: "C6H11O2"
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03684x"
- name: "Hexanoate (N-C6:0)"
- compartment: "x"
- formula: "C6H11O2"
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM02169e"
- name: "indoleacetate"
Expand Down Expand Up @@ -58633,14 +58625,6 @@
- charge: 0
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03684e"
- name: "Hexanoate (N-C6:0)"
- compartment: "e"
- formula: "C6H11O2"
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM01954c"
- name: "glcnac-alpha-1,4-core 1"
Expand Down Expand Up @@ -248691,25 +248675,6 @@
- subsystem:
- "Fatty acid oxidation"
- confidence_score: 0
- !!omap
- id: "MAR09949"
- name: "Acylcoa Hydrolase, Cytosolic"
- metabolites: !!omap
- MAM01597c: 1
- MAM02039c: 1
- MAM02040c: -1
- MAM02122c: -1
- MAM03684c: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "3.1.2.2"
- references: ""
- subsystem:
- "Fatty acid oxidation"
- confidence_score: 0
- !!omap
- id: "MAR09950"
- name: "Hydrolysis of Tetradecadienoyl Coenzyme A to Cis-5, 8-Tetradecadienoic Acid"
Expand Down Expand Up @@ -253804,16 +253769,16 @@
- confidence_score: 0
- !!omap
- id: "MAR10374"
- name: "Acyl-Coenzyme A Hydrolase, Mitochondrial"
- name: "Hexanoyl-CoA hydrolase, Mitochondrial"
- metabolites: !!omap
- MAM01597m: 1
- MAM02039m: 1
- MAM02040m: -1
- MAM02122m: -1
- MAM03684m: 1
- MAM02120m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: ""
- gene_reaction_rule: "ENSG00000123130"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
Expand Down Expand Up @@ -253855,16 +253820,16 @@
- confidence_score: 0
- !!omap
- id: "MAR10377"
- name: "Acylcoa Hydrolase, Peroxisome"
- name: "Hexanoyl-CoA hydrolase, Peroxisome"
- metabolites: !!omap
- MAM01597x: 1
- MAM02039x: 1
- MAM02040x: -1
- MAM02122x: -1
- MAM03684x: 1
- lower_bound: -1000
- MAM02120x: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: ""
- gene_reaction_rule: "ENSG00000101473"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
Expand Down Expand Up @@ -269331,8 +269296,8 @@
- id: "MAR11290"
- name: "Transport of Hexanoate (N-C6:0), Mitochondrial"
- metabolites: !!omap
- MAM03684c: 1
- MAM03684m: -1
- MAM02120c: 1
- MAM02120m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
Expand All @@ -269347,24 +269312,8 @@
- id: "MAR11291"
- name: "Transport of Hexanoate (N-C6:0), Peroxisome"
- metabolites: !!omap
- MAM03684c: 1
- MAM03684x: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR11292"
- name: "Transport of Hexanoate (N-C6:0), Extracellular"
- metabolites: !!omap
- MAM03684c: -1
- MAM03684e: 1
- MAM02120c: 1
- MAM02120x: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
Expand All @@ -269375,21 +269324,6 @@
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR11293"
- name: "Exchange of Hexanoate (N-C6:0)"
- metabolites: !!omap
- MAM03684e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- subsystem:
- "Exchange/demand reactions"
- confidence_score: 0
- !!omap
- id: "MAR11294"
- name: "Hydrolysis of Fatty Acyl Coenzyme A (14:1)"
Expand Down Expand Up @@ -302994,7 +302928,7 @@
- MAM02040c: -1
- MAM02554c: -1
- MAM02555c: 1
- MAM03684c: 1
- MAM02120c: 1
- MAM20037c: -1
- lower_bound: 0
- upper_bound: 1000
Expand Down
10 changes: 4 additions & 6 deletions model/metabolites.tsv
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Expand Up @@ -3651,8 +3651,10 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM02119l" "MAM02119" "6thf" "" "" "" "169691" "" "" "" "6thf" "MNXM3616" "m02119l" "m02119l"
"MAM02119m" "MAM02119" "6thf" "" "" "" "169691" "" "" "" "6thf" "MNXM3616" "m02119m" "m02119m"
"MAM02119e" "MAM02119" "6thf" "" "" "" "169691" "" "" "" "6thf" "MNXM3616" "m02119s" "m02119s"
"MAM02120c" "MAM02120" "" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" "m02120c" "m02120c"
"MAM02120e" "MAM02120" "" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" "m02120s" "m02120s"
"MAM02120c" "MAM02120" "hxa" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" "m02120c" "m02120c"
"MAM02120e" "MAM02120" "hxa" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653" "m02120s" "m02120s"
"MAM02120x" "MAM02120" "hxa" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653"
"MAM02120m" "MAM02120" "hxa" "C01585" "HMDB0000535" "CHEBI:17120;CHEBI:30776" "" "LMFA01010006" "" "" "caproic" "MNXM1653"
"MAM02121c" "MAM02121" "" "C05749" "" "" "" "" "" "HC01592" "HC01592" "MNXM23683" "m02121c" "m02121c"
"MAM02122c" "MAM02122" "" "C05270" "HMDB0002845" "CHEBI:27540" "440611" "LMFA07050001" "" "HC01409" "hxcoa" "MNXM162502;MNXM553" "m02122c" "m02122c"
"MAM02122m" "MAM02122" "" "C05270" "HMDB0002845" "CHEBI:27540" "440611" "LMFA07050001" "" "HC01409" "hxcoa" "MNXM162502;MNXM553" "m02122m" "m02122m"
Expand Down Expand Up @@ -6649,7 +6651,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM03814c" "MAM03814" "pchollinl_hs" "" "" "CHEBI:28733" "" "" "" "" "pchollinl_hs" "" "" "pchollinl_hs_c"
"MAM03856c" "MAM03856" "pelinl_hs" "" "" "CHEBI:83058" "" "" "" "" "pelinl_hs" "" "" "pelinl_hs_c"
"MAM03569c" "MAM03569" "eidi1114ac" "C16525" "HMDB0005060" "CHEBI:603631" "6439848" "" "" "" "eidi1114ac" "" "" "eidi1114ac_c"
"MAM03684c" "MAM03684" "hxa" "" "" "CHEBI:17120" "" "" "" "" "hxa" "MNXM1653" "" "hxa_c"
"MAM03976c" "MAM03976" "tetdeca511ac" "" "" "" "" "" "" "" "tetdeca511ac" "" "" "tetdeca511ac_c"
"MAM03619c" "MAM03619" "glyc2p" "" "" "CHEBI:58083" "" "" "" "" "glyc2p" "MNXM2527" "" "glyc2p_c"
"MAM03401c" "MAM03401" "aclys" "" "" "" "" "" "" "" "aclys" "" "" "aclys_c"
Expand Down Expand Up @@ -6792,8 +6793,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM03619e" "MAM03619" "glyc2p" "" "" "" "" "" "" "" "glyc2p" "MNXM2527" "" "glyc2p_s"
"MAM01998e" "MAM01998" "glyclt" "C00160" "HMDB0000115" "CHEBI:17497" "757" "" "" "" "glyclt" "MNXM222" "" "m01998s"
"MAM03232e" "MAM03232" "3hpppn" "" "" "" "" "" "" "" "3hpppn" "MNXM1634" "" "3hpppn_s"
"MAM03684m" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_m"
"MAM03684x" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_p"
"MAM02169e" "MAM02169" "ind3ac" "C00954" "HMDB0000197" "CHEBI:16411" "802" "" "" "" "ind3ac" "MNXM383" "" "m02169s"
"MAM02350e" "MAM02350" "Lcyst" "C00506" "HMDB0002757" "CHEBI:21260" "25701" "" "" "" "Lcyst" "MNXM713" "" "m02350s"
"MAM02413c" "MAM02413" "Lpipecol" "C00408" "HMDB0000716" "CHEBI:30913" "439227" "" "" "" "Lpipecol" "MNXM684" "" "m02413c"
Expand Down Expand Up @@ -7327,7 +7326,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM04078c" "MAM04078" "" "" "" "" "" "" "" "" "xolest204_hs" "" "" "xolest204_hs_c"
"MAM04080c" "MAM04080" "xolest226_hs" "" "" "" "" "" "" "" "xolest226_hs" "" "" "xolest226_hs_c"
"MAM02908e" "MAM02908" "sphmyln_hs" "C00550" "" "CHEBI:17636" "" "LMSP03010000" "" "HC02007" "sphmyln_hs" "MNXM5930" "" "m02908s"
"MAM03684e" "MAM03684" "hxa" "" "" "" "" "" "" "" "hxa" "MNXM1653" "" "hxa_s"
"MAM01954c" "MAM01954" "gncore1" "" "" "" "" "" "" "" "gncore1" "MNXM18091" "" "m01954c"
"MAM01954e" "MAM01954" "gncore1" "" "" "" "" "" "" "" "gncore1" "MNXM18091" "" "m01954s"
"MAM03394c" "MAM03394" "Lhcystin" "" "" "" "" "" "" "" "Lhcystin" "" "" "Lhcystin_c"
Expand Down
3 changes: 0 additions & 3 deletions model/reactions.tsv
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Expand Up @@ -9740,7 +9740,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR09946" "" "" "" "" "" "XOLEST204CEH" "" "" "" "" 0 "" "" "XOLEST204CEH"
"MAR09947" "" "XOLEST226CEH" "" "" "" "XOLEST226CEH" "" "" "" "" 0 "" "" "XOLEST226CEH"
"MAR09948" "" "CE4843HYDc" "" "" "" "CE4843HYDc" "" "" "" "" 0 "" "" "CE4843HYDc"
"MAR09949" "" "FACOAE60" "" "" "" "HXCOAc" "MNXR99139" "" "" "" 0 "" "" "HXCOAc"
"MAR09950" "" "TETDECA511ACc" "" "" "" "TETDECA511ACc" "" "" "" "" 0 "" "" "TETDECA511ACc"
"MAR09951" "" "GPDDACHOL" "" "" "" "GPDDACHOL" "" "" "" "" 0 "" "" "GPDDACHOL"
"MAR09952" "" "ACLYSHYc" "" "" "" "ACLYSHYc" "" "" "" "" 0 "" "" "ACLYSHYc"
Expand Down Expand Up @@ -10964,8 +10963,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR11289" "" "PHEACGLYtm" "" "" "" "PHEACGLYtm" "MNXR157011" "" "" "" 0 "" "" "PHEACGLYtm"
"MAR11290" "" "HXAt1" "" "" "" "HXAt1" "" "" "" "" 0 "" "" "HXAt1"
"MAR11291" "" "HXAt2" "" "" "" "HXAt2" "" "" "" "" 0 "" "" "HXAt2"
"MAR11292" "" "HXAt3" "" "" "" "HXAt3" "" "" "" "" 0 "" "" "HXAt3"
"MAR11293" "" "EX_hxa_e" "" "" "" "EX_hxa[e]" "MNXR98664" "" "" "" 0 "" "" "EX_hxa[e]"
"MAR11294" "" "TTDCEAc" "" "" "" "TTDCEAc" "" "" "" "" 0 "" "" "TTDCEAc"
"MAR11295" "" "PACCOALm" "" "" "" "PACCOALm" "" "" "" "" 0 "" "" "PACCOALm"
"MAR11296" "" "PACALDtm" "" "" "" "PACALDtm" "MNXR102312" "" "" "" 0 "" "" "PACALDtm"
Expand Down